[ensembl-dev] problem in variant effect predictor stand alone
Will McLaren
wm2 at ebi.ac.uk
Wed Feb 16 04:44:23 GMT 2011
Dear Ketyan,
Are you able to send me the input lines that are causing these errors? It is
difficult for me to diagnose the problem without seeing the data.
Thanks
Will
On 16 February 2011 13:08, ketan padiya <ketanmicro at gmail.com> wrote:
> Thanks for reply, It worked well.
>
> One more question for INDEL, variant_effect_predictor perl script don't
> recognize INDEL string and gives warning like,
>
> WARNING: Invalid allele string atggtccaatggtccaa/atggtccaa on line 92
> WARNING: Invalid allele string aaaa/aaa on line 1249
> WARNING: Invalid allele string cc/c on line 1378
>
>
>
> On Tue, Feb 15, 2011 at 6:37 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
>> Dear Ketyan,
>>
>> On 15 February 2011 20:13, ketan padiya <ketanmicro at gmail.com> wrote:
>>
>>> I have downloaded variant effect predictor and EnsEMBL API for that my
>>> problems are,
>>>
>>> 1) After every reboot of system i have to give the PERL5LIB path, Why?
>>>
>>
>> You can configure your system to load this PERL5LIB automatically every
>> time it starts. How you do this depends on what type of system you are
>> using. For example, if you are using the CSH shell system, you can edit the
>> file named ".cshrc" in your home directory, then add lines like:
>>
>> setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl/modules
>> setenv PERL5LIB ${PERL5LIB}:${HOME}/srcl/ensembl-compara/modules
>> setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl-functgenomics/modules
>> setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl-variation/modules
>>
>> Or, if you use Bash, you can add the lines to ".bashrc", also in your home
>> directory:
>>
>> PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-live
>> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules
>> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules
>> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules
>> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-functgenomics/modules
>> export PERL5LIB
>>
>>
>>
>>> 2) Variant effect predictor is taking too long to process given vcf file
>>> (~2000 line of SNP/INDELs)
>>>
>>
>> For this and point 3), I recommend you try adding the following flags to
>> your command:
>>
>> perl variant_effect_predictor.pl -i
>> ../samtools-0.1.12a/samfiles/q20/vcf/GKUNU9Q04_chr1_q20_sort.vcf -o chr1.txt
>> -format vcf -s cow -w -b 5000
>>
>> Using -format forces the program to read your file as a VCF.
>>
>> Using -w means the script runs in "whole-genome" mode, which is better
>> suited to large data sets that cover, for example, one chromosome. You
>> should make sure when you use this that the VCF input file is sorted by
>> chromosome and then position.
>>
>> Setting a larger buffer size with -b helps whole genome mode work faster.
>>
>> Please note that the -w option is only available from version 61 of
>> Ensembl.
>>
>> Thanks and good luck!
>>
>> Will McLaren
>> Ensembl Variation
>>
>>
>>
>>> 3) In the end it gives error,
>>>
>>> [orf at localhost variant_effect_predictor]$ perl
>>> variant_effect_predictor.pl -i
>>> ../samtools-0.1.12a/samfiles/q20/vcf/GKUNU9Q04_chr1_q20_sort.vcf -o chr1.txt
>>> -s cow
>>> WARNING: Start 5959615 or end . coordinate invalid on line
>>> 92 / INDEL
>>> WARNING: Start 30571012 or end . coordinate invalid on line 572
>>> / INDEL
>>> WARNING: Start 64306203 or end . coordinate invalid on line 819
>>> / INDEL
>>> WARNING: Start 76575493 or end . coordinate invalid on line 895
>>> / INDEL
>>> DBD::mysql::st execute failed: Lost connection to MySQL server during
>>> query at
>>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line
>>> 521, <GEN0> line 1006.
>>>
>>> -------------------- EXCEPTION --------------------
>>> MSG: Detected an error whilst executing SQL 'SELECT
>>> vf.variation_feature_id, vf.seq_region_id, vf.seq_region_start,
>>> vf.seq_region_end, vf.seq_region_strand, vf.variation_id, vf.allele_string,
>>> vf.variation_name, vf.map_weight, s.name, s.somatic,
>>> vf.validation_status, vf.consequence_type, vf.class_so_id
>>> FROM ( (variation_feature vf, source s)
>>> LEFT JOIN failed_variation fv ON fv.variation_id = vf.variation_id )
>>> WHERE s.somatic = 0 AND
>>> (
>>> fv.variation_id IS NULL OR
>>> fv.subsnp_id IS NOT NULL
>>> )
>>> AND vf.seq_region_id = 142972 AND vf.seq_region_start <= 23402307
>>> AND vf.seq_region_end >= 23402307 AND vf.seq_region_start >= 23401807 AND
>>> vf.source_id = s.source_id
>>> ': DBD::mysql::st execute failed: Lost connection to MySQL server during
>>> query at
>>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line
>>> 521, <GEN0> line 1006.
>>>
>>> STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch
>>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:522
>>> STACK Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_fetch
>>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm:495
>>> STACK
>>> Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_constraint
>>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm:316
>>> STACK
>>> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice_constraint
>>> /home/orf/EnsEMBL/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:121
>>> STACK
>>> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice
>>> /home/orf/EnsEMBL/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:175
>>> STACK main::print_consequences variant_effect_predictor.pl:318
>>> STACK toplevel variant_effect_predictor.pl:289
>>> Ensembl API version = 61
>>> ---------------------------------------------------
>>>
>>>
>>> --
>>> Ketan Padiya
>>> Research Fellow
>>> Anand Veterinary College
>>> Gujarat
>>> India.
>>> +91 9428969448
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list
>>> Dev at ensembl.org
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>
>>>
>>
>
>
> --
> Ketan Padiya
> Research Fellow
> Anand Veterinary College
> Gujarat
> India.
> +91 9428969448
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
>
>
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